s Indian Journal of Medical Microbiology 39 (2021) S1–S133 after 60 years of age as comorbidities also play a role. Methods:Reverse transcriptase Polymerase Chain Reaction testing (RT-PCR) was done on nasopharyngeal swab specimens from persons with respiratory illness attending at SRRIT & CD Hyderabad during 6 months period from May 2020 to October 2020. Results:A total of 4617 samples were tested by RT-PCR of which 1722(37%) shows positive results for COVID-19. 1056 (61.3%) were males and 666 (38.7%) were females. Highest positive rate was noted in month of June 528(11.4%) followed by July, August, September & October which are 8.6%, 6.8%. 5.3%, 3.2% respectively. Male preponderance was seen in 31-45 years of age group while it is 16-30 years in females. Conclusions:The clinical features and prognosis of the disease vary among patients of different ages and a thorough assessment of age may help clinicians to establish risk stratification for all COVID-19 patients https://doi.org/10.1016/j.ijmmb.2021.08.222 PREVALENCE OF COVID 19 IN NORTH CHENNAI-A CROSS SECTIONAL STUDY Abirami Amirthalingam, D.I.L.L.I.R.A.N.I. VEDHACHALAM, V. SHEEBA, V. INDUMATHI. Government Stanley Medical College Background: SARS CoV 2 is a new Beta coronavirus subgenus Sarbecovirus, family Coronaviridae Causing pandemic of coronavirus disease 2019(COVID 19) It spread rapidly causing severe global public health crisis. Transmitted mainly by respiratory droplets, it causes atypical pneumonia and acute respiratory distress syndrome. RT PCR is the recommended test by ICMR for surveillance of COVID 19. According to WHO total cases in India is around 8.96million and deaths around 1, 32000(2%). Methods:Nasopharyngeal and oropharyngeal swabs collected over a period of 8 months from April to November 2020 were subjected to RT PCR by ICMR approved RTPCR kits. Results: Among 1, 84,915 samples tested, 19,431 (10.5%) were positive for COVID 19 and 1, 64,802 (89.14%) were negative. 682 samples (0.36%) were rejected out of which 132(0.07%) were rejected pre analytically and 550 (0.29%) post analytically. Males (64%) were affected more than females (36%). Peak incidence was found between 20 -40 years of age (73%) and Co-morbidity in 15% of cases. Maximum Positivity rate of 29.8%was observed in June and thereafter a steady decline was observed. Conclusions: This study conducted in North Chennai recognized as Red zone of Tamil Nadu in April 2020shows a gradual increase in positive cases with peaking in June 2020(29.8%) unlike the peaking seen in September in rest of India. A steady decline to 4.1% was noted in the following months. Due to effective containment measures of Government by legally mandated quarantine, active surveillance of cases and controls with early diagnosis and isolation, barricading of hotspots, mandatory face masks, social distancing ,hand sanitation and cough etiquette, positivity rate declined in the last 4 months even after lifting the lockdown. The challenges we face in diagnosis and treatment of COVID19 emphasize the need to promote research and development, strengthening drug and vaccination development programs and evolving a robust action plan to face a pandemic. https://doi.org/10.1016/j.ijmmb.2021.08.219 THE IMPORTANCE OF CYCLE THRESHOLD VALUES IN DETECTION OF SEVERITY & OUTCOME IN PATIENTS WITH SARS-COV-2 B.R. Archana, S. Sangeetha. Rajarajeswari Medical College & Hospital Background:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly transmissible and pathogenic coronavirus that emerged in late 2019 and has caused a devastating pandemic of acute respiratory disease, named ‘coronavirus disease 2019’ (COVID-19). This pandemic caused health problems of human beings and an economic decline worldwide. The real-time reverse S64 transcription (rRT)-polymerase chain reaction (PCR) assay by a naso & oropharyngeal swab is effective for diagnosis of COVID-19, it is considered that cycle threshold value (Ct-value) of rRTPCR assay inversely correlated with viral load and are not reported clinically. So this study was undertaken retrospectively to compare Ct values of patients tested positive for SARS CoV 2 by rRT-PCR with severity of illness, duration of hospital & mortality. Methods:A retrospective study was performed among patients tested positive for SARS CoV 2 by rRTPCR& admitted in Rajarajeswari medical college& hospital, Bangalore. The details of the patients on duration of hospital stay, age, presence of comorbidities, intubation, mortality was collected. The Ct values of rRT-PCR test was compared with severity & mortality of illness. The data was analyzed using descriptive statistics. Results:The study comprised of 100 patients tested positive for SARS CoV 2 by rRTPCR. The Ct values were compared with duration of hospital stay, severity of illness & mortality. The patients with low Ct values were associated with increased duration of hospital stay, severity of illness. Low Ct values were also associated with increased age & presence of other comorbidities. Conclusions:Ct values of SARS-CoV-2 rRT-PCR among hospitalized patients with COVID-19 independently correlates with the severity of illness and duration of hospitalization. Providing this information to clinicians could potentially be used t o guide patient care. https://doi.org/10.1016/j.ijmmb.2021.08.220 CRP WAS FOUND TO BE AN INDEPENDENT DISCRIMINATOR IN COVID19 PATIENTS K. Bhagya, E. Subbalakshmi, B. Kalpana Devi. ACS Medical College and Hospital, Chennai Background: The outbreak of novel Coronavirus Disease 2019 has led to the pandemic. This virus is causing severe acute respiratory syndrome, with increasing morbidity and mortality and yet to find a vaccine for the virus. Several inflammatory markers help in early pickup of severely affected patients. One of the inflammatory marker is C reactive protein. Methods: A prospective study was done from Sep 2020 to Nov 2020. We collected 200 samples from inpatients in COVID wards. CRP was done by passive agglutination test, and the positive value was expressed in mg/L. Results: After statistical analysis, Out of 200 COVID positive patients 71 were >60 years of age, 56 were 41-60 years of age, and 22 were in 19-40 years of age group. There were no patients below 19 years of age in our hospital. Positive CRP value was present around 36% in age group of >60 years of age group, 28% in 41-60 age group and 11% in 19-40 years of age group. Conclusions: In patients with COVID-19, CRP has correlated with the advancing age group, also tended to be a good predictor of adverse outcome https://doi.org/10.1016/j.ijmmb.2021.08.221

Background:The isolation of S. pneumoniae (Sp) depends on specimen integrity / transport, media and expertise. The non-availability of sheep blood agar poses a challenge in identification of colonial morphology and identification in India.Methods:Laboratories processed swabs containing either pure Sp or Sp in mixed cultures with a second (confounding) bacterium shipped across the country in cold conditions. Duplicate set of swabs was shipped back to the central laboratory to assess the impact of shipping on culture viability. The identical swab was cultured on sheep, human blood and one additional agar plate used in the laboratory.Results:46/60(77%) of cultures containing only Sp were correctly identified. In specimens where Sp was present in mixed culture, the proportion of isolates in which Sp was correctly identified varied, with most variability attributed to the particular confounding organism rather than the media. There was no discernible impact of temperature-controlled (4-6°C) transport on the isolation of Sp from culture swabs.Conclusions:The study clearly elucidates the ability of laboratories for isolation of S. pneumoniae on human blood agar in resource limited settings. The results highlight the difficulties inherent in correctly identifying pathogens in mixed cultures in needs improvement using standardized tests across the study centers. The study also reaffirms the ability to transport biological specimens over long geographical distances without loss.

Coagulase-negative staphylococci (CoNS) have been increasingly recognized as a clinically important group of species that can cause several opportunistic nosocomial infections. There are at least 47 known species of Staphylococci and to differentiate all these species >40 biochemical tests need to be performed. The present study was able to refine the CoNS identification process by using only five tests to identify S. epidermidis from the rest and used six other tests to identify eleven other clinically significant CoNS species. A total of 242 CoNS isolates were collected from tertiary care hospitals and included in the study. The five-biochemical test scheme devised based on mathematical probability derived from a computer algorithm included fermentation of mannitol, maltose, mannose, trehalose and novobiocin susceptibility to differentiate S. epidermidis from other CoNS species. The remaining CoNS isolates other than S. epidermidis were further characterized with the help of six additional tests, which identified another eleven species. Species-specific PCR and 16SrDNA sequencing were used to confirm and validate the identification scheme. Species-specific PCR and 16SrDNA sequencing showed 100% agreement with non-divergent phenotypic test results, indicating that the five selected assays are highly specific for identifying S. epidermidis. In conclusion, this study used only 11 tests to identify most of the clinically significant CoNS that can reduce cost and time. This scheme is easy to perform in any laboratory with basic resources, the results of this study were validated using more accurate molecular methods such as PCR and 16S rDNA typing to confirm the utility of the proposed scheme.

Periodontitis is a chronic inflammation of the periodontium which progresses to bone resorption and tooth loss in the event of delayed or lack of treatment. Chronic periodontitis is recognized as the most frequently occurring form of periodontitis which is mainly attributed to the presence of Gram negative anaerobic organisms in the sub gingival plaque of these patients. However there are wide differences in the proportion of type of microorganisms in different geographical areas attributed to ethnicity, dietary habits and socio economic status. So the study of sub gingival microbiota in a particular country becomes relevant for understanding their implications in the pathogenesis of periodontal disease and also to identify their possible impact on treatment outcomes. As there is a paucity of information on the prevalence of Gram negative anaerobic micro organisms in our population, the present study was under taken to isolate and identify the Gram negative anaerobic bacilli. This cross sectional study was carried out between January and December 2013 on 71 chronic periodontitis and 55 healthy subjects attending the dental outpatient department of our tertiary care hospital. The sub gingival plaque samples were processed using anaerobic culture to isolate obligate anaerobic Gram negative bacilli. Identification was performed using special potency antimicrobial discs and standard biochemical reactions. 71.84% in chronic periodontitis and 50.91% in healthy participants showed the presence of obligate anaerobic Gram negative bacilli. Porphyromonas (13.18%), Prevotella (32.97%), Bacteroides (24.17%) and Fusobacterium (29.67%) were isolated in chronic periodontitis while Porphyromonas (8.69%), Prevotella (30.43%), Bacteroides (26.08%) and Fusobacterium (34.78%) were isolated from the control group. The proportion of these putative pathogens was found to be higher in chronic periodontitis patients when compared to healthy subjects. The presence of anaerobic Gram negative bacilli in both study groups points towards the possibility of an opportunistic role that these organisms assume in the presence of risk factors.

Carbapenemases are β-lactamases that confer resistance to almost all β-Lactam antibiotics. There is an urgent need for identification of these enzymes. The main aim of this study includes to detect different Carbapenemase enzymes produced by Enterobacteriacae among clinical isolates using phenotypic tests. Isolates from various clinical samples that showed resistance to Imipenem and/or Meropenem by Kirby Bauer disc diffusion method were analysed over a period of 6 months. These isolates were screened using Modified Hodge test (MHT), KPC CHROM agar, and supplemental tests such as Blue Carba Test (BCT) and Inhibitor Based Phenotypic Test (IBPT) were done to detect different Carbapenemase enzymes. 60 out of 430 (13.95%) strains were Carbapenem resistant Enterobacteriacae. Among the 4 tests performed MHT detected Carbapenemases in 36.6% and KPC CHROM agar in 96.6% isolates. Blue Carba Test showed 13.3% isolates as KPC/MBL phenotype and 3.3% as OXA phenotype. Inhibitor Based Phenotypic Test detected 8.3% isolates as KPC producers and 5% as MBL producers. Among these four phenotypic tests KPC CHROM agar could be useful as a screening test for Carbapenemase detection, BCT and IBPT would be useful to differentiate these Carbapenemases.

INTRODUCTION:Haemodialysis is one of the treatment modalities for patients suffering from end stage renal disease (ESRD). Dialysis patients are exposed to large volumes of water for production of dialysis fluids. Treated water and dialysate come in direct contact with the patient's bloodstream. Such patients suffer from abnormalities of the immune system, making them more susceptible to infections. Microbial contamination of the treated water and dialysate can lead to biofilm formation and release of endotoxins in Haemodialysis system. These can give rise to pyrogenic reactions in the short term and β2 amyloidosis, atherosclerosis, and increased mortality in the long term.AIM:To assess the bacteriological quality of treated water and dialysate used in the Haemodialysis unit of a tertiary care hospital.MATERIALS AND METHODS:A retrospective review of records of treated water and dialysate samples sent to the Microbiology laboratory for analysis of bacteriological contamination of the water used in haemodialysis treatment from January 2013 to June 2014 was conducted. The acceptable limits for treated water and dialysate were taken as <200 CFU/ml and < 2000 CFU/ml respectively as per Government of India Guidelines for Maintenance Haemodialysis.RESULTS:Thirty six samples of treated water and 394 samples of dialysate were analysed for bacteriological contamination. 4 out of 36 (11.1%) samples of treated water and 44 out of 394 dialysate samples (11.2%) showed unacceptable bacteriological growth.CONCLUSION:Regular and continual monitoring of the disinfection protocol of the water distribution system in haemodialysis unit is necessary to get good microbiological quality of treated water and dialysate fluid.

Corynebacterium pseudodiphtheriticum is a common commensal flora of the upper respiratory tract in humans. Though the pathogenicity of C. pseudodiphtheriticum is not rare, its role as an opportunistic pathogen is mainly limited to the lower respiratory tract, particularly in patients with underlying systemic conditions or immune-compromisation. We hereby present the first case of C. pseudodiphtheriticum causing diphtheria-like illness affecting the upper respiratory tract of a 6-year-old fully immunised otherwise healthy child. In countries with very low incidence of diphtheria, C. pseudodiphtheriticum should be included in differential diagnosis for a child presenting with diphtheria-like illness. Simple, rapid screening tests should be used to differentiate it from C. diphtheriae and hence, to prevent unnecessary concern in community.

UNLABELLED Necrotising Soft Tissue Infection is a rapidly progressing fatal disorder, the prognosis of which depends on early diagnosis and management. OBJECTIVE In this study, our objective was to assess the factors contributing to mortality due to NSTI. METHODS A retrospective review of the records of all patients with NSTI involving fascia, skin or muscle between January 2007 and December 2011, was performed. The atiology, predisposing factors, risk factors, causative microbiological organisms and the clinical outcomes associated with mortality were studied. Statistical Data: Descriptive statistics comprising of proportion(%) presented. Chi-square test was employed to assess the statistical significance in the distribution of various known risk factors between the survivors and non-survivors. A 'p' value less than 0.05 was considered significant. RESULTS Sixty patients records were reviewed. Fifty-one patients (85%) were males and nine (15%) were females. Mean age was 46.57 years (+/- 20.60) ranging from 15-83 years. All the patients were treated by debridement & wide spectrum antibiotics. Mono-microbial atiology being found in 27 patients (63.3%) and polymicrobial culture was isolated in 13 patients (36.7%), with E-coli and staphylococci being the most common organisms to be isolated. In most patients, multiple debridements were done. The overall mortality rate was estimated to be 25%. Age, aatiology, diabetes mellitus, hypoalbuminemia, alcohol, site of infection, bacteriology etc. were the risk factors associated with mortality, that were evaluated. Diabetes mellitus was the most common associated risk factor found in 32 patients (53.3%), though not statistically significant. Increasing age (>50 years, p value = 0.016), raised Serum Creatinine (>1.2mg/dl, p-value = 0.023) and delayed surgical intervention(>24 hours p value= 0.006) were the risk factors associated with Mortality in NSTI that were statistically significant. CONCLUSION Despite the use of appropriate antibiotic treatment, aggressive debridement & resuscitation, NSTI still leads to a high mortality & morbidity. In this series, there is high mortality associated with increasing age, raised serum creatinine and delayed surgical intervention. The mortality rate (25%) is comparable with other studies.

Between May and June 2002, we recorded an outbreak of Septic Arthritis in neonates due to Extended Spectrum ß-Lactamase producing Klebsiella pneumoniae at our neonatal intensive care unit.The confirmed cases were then followed up to look for long term morbidities associated with the infection.We analyzed the microbiological and epidemiological features of the outbreak and the various measures implemented to ward off the same.We also studied the long term morbidities associated with nosocomial infection.All neonates admitted to the NICU during this period were screened and those with clinico-microbiological evidence of septic arthritis were included in the study.Microbiological screening of the environment, personnel, patients and their attendants were conducted and 85 different environmental sites were sampled.Six neonates were confirmed to have septic arthritis after an average NICU stay of 10.00±3.16days.Culture of synovial fluid grew K. pneumoniae.All isolates had similar biochemical and antibiotic resistance pattern suggestive of clonality of infection.Plasmid analysis of these samples revealed a single plasmid (35.8MD) in all the isolates.Similar K. pneumoniae strain with the same plasmid was isolated from the water samples which was stored

We report a case of fungal retinal vasculitis in a 32 week gestational age, 1200 g premature infant detected during routine screening for retinopathy of prematurity at 78 days of age. The patient subsequently developed sepsis with perinephric abscess but responded rapidly to systemic therapy. Fortuitous detection of retinal vasculitis as the first evidence of a systemic fungal infection in an immunocompetent and asymptomatic infant has not, to our knowledge, been previously reported.

Context: Knowledge of microbiology and antibiotic susceptibility of complicated urinary tract infection (cUTI) is essential for defining the empirical treatmentAims: 1) To find out the common presenting symptomatology associated with cUTI 2) To determine the distribution of bacterial strains isolated from cUTI 3) To identify Extended Spectrum Beta Lactamase (ESBL) producers in the different populations of uropathogens 4)To determine the resistance pattern of these bacteria. Settings and Design: Prospective study was done in a tertiary care centre in Bangalore from l January, 2008 to 31st December, 2008. Methods and Material: The study included all the patients who were admitted or visited the outpatient departments in the hospital and had urinary tract infection confirmed by positive urine culture reports. Results: Dysuria (31.4%) was the most common symptom with cUTI patients. Escherichia coli accounted to 65.7% of the total infection. 66.78% of the total Escherichia coli were ESBL positive. A high degree of resistance was recorded for first generation fluoroquinolones (76.9%) among the isolates in our study. Conclusions: A unified antibiotic protocol is necessitated to limit this increase and reduce the squeal of cUTI.

To the best of our knowledge, injection abscess due to Salmonella typhi has not been reported earlier. A patient with fever of unknown origin was diagnosed as suffering from typhoid fever, administered a course of ceftrioxone but patient developed an injection abscess due to S. typhi, abscess was drained and patient was started on ciprofloxacin to which he responded favourably.

We report a case of nocardiosis in an immunosuppressed elderly patient who presented with prolonged pyrexia. Nocardia asteroides was isolated from the thyroid, with CT scan evidence of dissemination to the brain, abdomen and lungs. The patient succumbed to illness despite aggressive therapy. Autopsy could not be performed. To the best of our knowledge, this is the first reported case from India, on Nocardia asteroides affecting the thyroid tissue.

Injection abscess is an iatrogenic infection occurring as an isolated case or as cluster outbreak. These infections occur due to contaminated injectables or lapse in sterilisation protocol. While pathogens such as Pseudomonas, Klebsiella, E. coli, and S. aureus are the usual causative agents, unusual organisms such as mycobacteria, particularly the rapidly growing non-tuberculous mycobacteria (NTM) may cause the abscess. The chances of overlooking these organisms is high unless an acid fast bacilli (AFB) smear and culture is done on all aspirated pus specimens. We report a case of a three year old child who presented with a gluteal abscess following an intramuscular infection with an unknown preparation.

This study sought to determine whether dip stick strip test containing antibody for Plasmodium falciparum histidine rich protein-II (PfHRP-II) antigen could be used for identification of P. falciparum and P. vivax malaria in man. The results obtained were also compared with the results of standard microscopic examination. A total of 150 cases were included for the study. Fifty cases were non-febrile cases with no history of malaria acting as control group and the rest 100 cases were having fever and formed the test group. All the cases in the control group was found to be negative for both microscopic examination and strip test. In the test group, all samples that showed positive for P. falciparum by microscopy was also found to be positive for strip test. Whereas, all those samples that were positive for P. vivax in microscopic examination was found to be negative for strip test indicating species specificity of the strip test. In addition, two other cases that were negative for microscopic examination were found to be positive for the strip test. Statistical analysis was done to compare the validity of the results of strip test with that of the results of microscopic examination.